Optical Genome Mapping as an Alternative to FISH-Based Cytogenetic Assessment in Chronic Lymphocytic Leukemia

Abstract

The fluorescence in situ hybridization (FISH) technique plays an important role in the risk stratification and clinical management of patients with chronic lymphocytic leukemia (CLL). For genome-wide analysis, FISH needs to be complemented with other cytogenetic methods, including karyotyping and/or chromosomal microarrays. However, this is often not feasible in a diagnostic setup. Optical genome mapping (OGM) is a novel technique for high-resolution genome-wide detection of structural variants (SVs), and previous studies have indicated that OGM could serve as a generic cytogenetic tool for hematological malignancies. Herein, we report the results from our study evaluating the concordance of OGM and standard-of-care FISH in 18 CLL samples. The results were fully concordant between these two techniques in the blinded comparison. Using in silico dilution series, the lowest limit of detection with OGM was determined to range between 3 and 9% variant allele fractions. Genome-wide analysis by OGM revealed additional (>1 Mb) aberrations in 78% of the samples, including both unbalanced and balanced SVs. Importantly, OGM also enabled the detection of clinically relevant complex karyotypes, undetectable by FISH, in three samples. Overall, this study demonstrates the potential of OGM as a first-tier cytogenetic test for CLL and as a powerful tool for genome-wide SV analysis.

A framework for the clinical implementation of optical genome mapping in hematologic malignancies

“…21 For in silico LLOD determination, the laboratory can use two samples, one with several abnormalities (preferably with different SV classes) and a normal control, and then down sample the molecule files (.bnx) in different proportions to represent the various "dilutions." 19 This process will demonstrate the limits of the assembly pipeline to detect low-level events. Please note that the LLOD is also dependent on variables such as quality of DNA (N50 >150 kb, map rate, coverage, CNA-tool/SV-tool), and coverage (see Section 3 for further detail).…”

“…These include a general assessment of OGM in various hematologic malignancies [8][9][10][11] as well as focused evaluations in specific patient cohorts such as Acute Myeloid Leukemia (AML), 12 Pediatric AML, 13 Myelodysplastic Syndromes, 14 Acute Lymphoblastic Leukemia, [15][16][17] and Chronic Lymphocytic Leukemia. 18,19 These studies have all demonstrated that OGM has equal or better sensitivity and resolution for the detection of diagnostic and prognostic abnormalities in hematologic malignancies with relatively few discordances. As such, clinical laboratories are now pursuing OGM for detection of sentinel cytogenomic abnormalities in patients with hematological neoplasms.…”

“…Several recent publications have compared the performance of OGM to standard cytogenetic approaches. These include a general assessment of OGM in various hematologic malignancies 8–11 as well as focused evaluations in specific patient cohorts such as Acute Myeloid Leukemia (AML), 12 Pediatric AML, 13 Myelodysplastic Syndromes, 14 Acute Lymphoblastic Leukemia, 15–17 and Chronic Lymphocytic Leukemia 18,19 . These studies have all demonstrated that OGM has equal or better sensitivity and resolution for the detection of diagnostic and prognostic abnormalities in hematologic malignancies with relatively few discordances.…”

Mapeo óptico del genoma: fundamentos tecnológicos y aplicaciones en neoplasias hematológicas

“…Diversas publicaciones recientes han demostrado que el OGM es una buena alternativa como prueba de primera línea para la detección de alteraciones cromosómicas en diferentes neoplasias hematológicas 7,11,14 , principalmente en la leucemia mieloide aguda (LMA) 8,12 , los síndromes mielodisplásicos (SMD) 8,17 , la leucemia linfoblástica aguda (LLA) 5,6,10 y la leucemia linfática crónica (LLC) 9,13 (Tabla 3). No obstante, todavía no se han publicado guías internacionales que especifiquen cuándo sería recomendable priorizar esta tecnología frente a los métodos convencionales (cariotipo, FISH, microarrays genómicos) y en qué afecciones la aplicación del OGM supondría una mejora en el manejo de los pacientes.…”

“…La tecnología de OGM ha sido probada con éxito en el análisis citogenómico de diferentes neoplasias hematológicas [5][6][7][8][9][10][11][12][13] . Numerosos estudios de validación han demostrado que, con una cobertura mínima de 400X, el OGM puede llegar a alcanzar una sensibilidad máxima cercana al 1%, una especificidad del 100% y un valor predictivo positivo superior al 80%.…”